[cig-commits] r18592 - in short/3D/PyLith/trunk: doc/userguide/tutorials/subduction doc/userguide/tutorials/subduction/figs examples/2d/subduction
brad at geodynamics.org
brad at geodynamics.org
Sat Jun 11 20:43:51 PDT 2011
Author: brad
Date: 2011-06-11 20:43:50 -0700 (Sat, 11 Jun 2011)
New Revision: 18592
Added:
short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/figs/cartoon_general.eps
short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/figs/step01.eps
short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/figs/step01_soln.png
short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/figs/step02.eps
short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/figs/step03.eps
short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/figs/subduction_tri3.png
Modified:
short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/figs/cartoon.svg
short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/figs/cartoon_general.svg
short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/subduction.lyx
short/3D/PyLith/trunk/examples/2d/subduction/geometry.jou
short/3D/PyLith/trunk/examples/2d/subduction/mesh_tri3.exo
short/3D/PyLith/trunk/examples/2d/subduction/pylithapp.cfg
short/3D/PyLith/trunk/examples/2d/subduction/step01.cfg
Log:
Changed subduction zone example to HDF5 output. More work on subduction zone example in manul.
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/figs/cartoon.svg
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/figs/cartoon.svg 2011-06-12 02:11:10 UTC (rev 18591)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/figs/cartoon.svg 2011-06-12 03:43:50 UTC (rev 18592)
@@ -644,7 +644,7 @@
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inkscape:label="Annotation (coseismic)"
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@@ -663,7 +663,7 @@
style="fill:none;stroke:#c90003;stroke-width:2;stroke-linecap:butt;stroke-linejoin:miter;stroke-miterlimit:4;stroke-opacity:1;stroke-dasharray:none;marker-end:url(#Arrow2MendL)" />
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<g
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+ style="display:none"
inkscape:label="Annotation (interseismic)"
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inkscape:label="BC (coseismic only)"
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@@ -960,7 +960,7 @@
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inkscape:label="Annotation (step01)"
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xml:space="preserve"
@@ -978,7 +978,7 @@
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Added: short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/figs/cartoon_general.eps
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/figs/cartoon_general.eps (rev 0)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/figs/cartoon_general.eps 2011-06-12 03:43:50 UTC (rev 18592)
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+0.788235 0 0.0117647 rg
+BT
+11.2 0 0 11.2 10 174.000006 Tm
+/f-0-0 1 Tf
+[<0102>-1<03>-1<04>-1<05>-1<06>-1<07>-1<02>-1<08>27<090a>1<0b0a040c0d0e
+0f>1<0a1003>-1<11>]TJ
+ET
+Q Q
+showpage
+%%Trailer
+count op_count sub {pop} repeat
+countdictstack dict_count sub {end} repeat
+cairo_eps_state restore
+%%EOF
Added: short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/figs/subduction_tri3.png
===================================================================
(Binary files differ)
Property changes on: short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/figs/subduction_tri3.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Modified: short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/subduction.lyx
===================================================================
--- short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/subduction.lyx 2011-06-12 02:11:10 UTC (rev 18591)
+++ short/3D/PyLith/trunk/doc/userguide/tutorials/subduction/subduction.lyx 2011-06-12 03:43:50 UTC (rev 18592)
@@ -102,6 +102,10 @@
Variable mesh resolution
\end_layout
+\begin_layout Itemize
+AREPRO programming language
+\end_layout
+
\end_deeper
\begin_layout Itemize
Linear triangular cells
@@ -187,7 +191,7 @@
\end_inset
- shows the three step of increasing complexity.
+ shows the three steps of increasing complexity.
Step 1 focuses on the coseismic slip, Step 2 focuses on interseismic deformatio
n, and Step 3 combines the two into a pseudo-earthquake cycle deformation
simulation.
@@ -203,7 +207,7 @@
\begin_layout Plain Layout
\align center
\begin_inset Graphics
- filename figs/twotri3-mesh.eps
+ filename figs/cartoon_general.eps
\end_inset
@@ -214,7 +218,7 @@
\begin_inset Caption
\begin_layout Plain Layout
-Cartoon of subduction zone with nonplanar fault geometry and topography.
+Cartoon of subduction zone example.
\begin_inset CommandInset label
LatexCommand label
name "fig:tutorial:subduction:overview"
@@ -242,19 +246,104 @@
\begin_layout Plain Layout
\align center
+\begin_inset Tabular
+<lyxtabular version="3" rows="2" columns="3">
+<features tabularvalignment="middle">
+<column alignment="center" valignment="top" width="0">
+<column alignment="center" valignment="top" width="0">
+<column alignment="center" valignment="top" width="0">
+<row>
+<cell alignment="center" valignment="top" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Step 1
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Step 2
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Step 3
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
\begin_inset Graphics
- filename figs/twotri3-mesh.eps
+ filename figs/step01.eps
+ lyxscale 66
+ width 2in
\end_inset
\end_layout
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" usebox="none">
+\begin_inset Text
+
\begin_layout Plain Layout
+\begin_inset Graphics
+ filename figs/step02.eps
+ lyxscale 66
+ width 2in
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+\begin_inset Graphics
+ filename figs/step03.eps
+ lyxscale 66
+ width 2in
+
+\end_inset
+
+
+\end_layout
+
+\end_inset
+</cell>
+</row>
+</lyxtabular>
+
+\end_inset
+
+
+\end_layout
+
+\begin_layout Plain Layout
\begin_inset Caption
\begin_layout Plain Layout
-Diagram of steps and boundary conditions in subduction zone tutorial.
+Diagram of fault slip and boundary conditions for each step in the subduction
+ zone tutorial.
\begin_inset CommandInset label
LatexCommand label
name "fig:tutorial:subduction:steps"
@@ -279,16 +368,28 @@
\end_layout
\begin_layout Standard
-ADD STUFF HERE
+We construct the mesh in Cubit by constructing the geometry, prescribing
+ the discretization, runnig the mesher, and then grouping cells and vertices
+ for boundary conditions and materials.
+ We use the APREPRO programming language within the journal files to enable
+ use of units and setting variables for values used many times.
+ An appendix in the Cubit documentation discusses the features available
+ with APREPRO in Cubit.
+ The Cubit commands are in three separate journal files.
+ The main driver is in the journal file mesh_tri3.jou.
+ It calls the journal file geometry.jou to construct the geometry and createbc.jou
+ to setup the groups associated with boundary conditions and materials.
+ The journal files are documented and describe the various steps outlined
+ below.
\end_layout
\begin_layout Enumerate
-Create geometry.
+Create the geometry defining the domain.
\end_layout
\begin_deeper
\begin_layout Enumerate
-Create point.
+Create points.
\end_layout
\begin_layout Enumerate
@@ -296,7 +397,8 @@
\end_layout
\begin_layout Enumerate
-Split curves to form bounding curves.
+Split curves to separate them into sections bounding surfaces.
+
\end_layout
\begin_layout Enumerate
@@ -343,7 +445,9 @@
\begin_layout Plain Layout
\align center
\begin_inset Graphics
- filename figs/twotri3-mesh.eps
+ filename figs/subduction_tri3.png
+ lyxscale 50
+ width 3in
\end_inset
@@ -381,20 +485,22 @@
\end_layout
\begin_layout Standard
-ADD STUFF HERE
-\end_layout
-
-\begin_layout Standard
-The settings contained in
+As in the examples discussed in previous sections of these tutorials, we
+ place parameters common to among the three steps in the
\family typewriter
pylithapp.cfg
\family default
+ file so that we do not have to duplicate them for each step.
+ The settings contained in
+\family typewriter
+pylithapp.cfg
+\family default
for this problem consist of:
\end_layout
\begin_layout Description
-pylithapp.journal.info Settings that control the verbosity of the output for
- the different components.
+pylithapp.journal.info Settings that control the verbosity of the output written
+ to stdout for the different components.
\end_layout
\begin_layout Description
@@ -416,45 +522,36 @@
\end_layout
\begin_layout Description
-pylithapp.petsc PETSc settings to use for the problem, such as the preconditioner
- type.
+pylithapp.problem.formuation.output Settings related output of the solution
+ over the domain and subdomain (ground surface).
\end_layout
-\begin_layout Standard
-All of the problems in this directory use the same material database, as
- specified under
+\begin_layout Description
+pylithapp.timedependent.materials.
+\shape italic
+MATERIAL
+\shape default
+.output Settings related to output of the state variables for material
+\shape italic
+MATERIAL
+\shape default
+.
\end_layout
-\begin_layout LyX-Code
-
-\family typewriter
-pylithapp.timedependent.materials
-\family default
-
+\begin_layout Description
+pylithapp.petsc PETSc settings to use for the problem, such as the preconditioner
+ type.
\end_layout
\begin_layout Standard
-in
-\family typewriter
-pylithapp.cfg
-\family default
-.
- This information is contained in the file
-\family typewriter
-matprops.spatialdb
-\family default
-.
- Although the material model is specified in
-\family typewriter
-pylithapp.cfg
-\family default
-, the values for the physical properties of the material are given in
-\family typewriter
-matprops.spatialdb
-\family default
-.
- For this example, values describing elastic plane strain material properties
- are given at a single point, resulting in uniform material properties.
+The physical properties for each material are specified in spatial database
+ files.
+ For example, the elastic properties for the continental crust are in mat_concru
+st.spatialdb.
+ The provided spatial database files all use just a single point to specify
+ uniform physical properties within each material.
+ A good exercise is to alter the spatial database files with the physical
+ properties to match PREM.
\end_layout
\begin_layout Subsection
@@ -462,166 +559,101 @@
\end_layout
\begin_layout Standard
-The first example problem is extension of the mesh along the diagonal extending
- from the lower left to the upper right of the square mesh.
- Parameter settings that augment those in
+The first example problem is earthquake rupture involving coseismic slip
+ along the interface between the subducting slab and the continental crust
+ and upper most portion of the mantle below the continental crust.
+ The spatial variation of slip comes from a cross-section of Gavin Hayes
+ finite-source model
+\begin_inset Flex URL
+status collapsed
+
+\begin_layout Plain Layout
+
+earthquake.usgs.gov/earthquakes/eqinthenews/2011/usc0001xgp/finite_fault.php
+\end_layout
+
+\end_inset
+
+.
+ On the lateral and bottom boundaries of the domain, we fix the degrees
+ of freedom perpendicular to the boundary as shown in Figure
+\begin_inset CommandInset ref
+LatexCommand ref
+reference "fig:tutorial:subduction:steps"
+
+\end_inset
+
+.Parameter settings that augment those in
\family typewriter
pylithapp.cfg
\family default
are contained in the file
\family typewriter
-axialdisp.cfg
+step01.cfg
\family default
.
These settings are:
\end_layout
\begin_layout Description
-pylithapp.timedependent Specifies an implicit formulation for the problem
- and specifies the array of boundary conditions.
+pylithapp.timedependent Specifies the array of boundary conditions.
\end_layout
\begin_layout Description
-pylithapp.timedependent.bc.bc Defines which degrees of freedom are being constraine
-d (x and y), gives the label (defined in
+pylithapp.timedependent.bc.
+\shape italic
+BOUNDARY
+\shape default
+ Defines the settings for boundary
+\shape italic
+BOUNDARY
+\shape default
+, including which degrees of freedom are being constrained (x or y), the
+ label (defined in
\family typewriter
-twotri3.mesh
+ mesh_tri3.exo
\family default
-) defining the points desired, assigns a label to the boundary condition
- set, and gives the name of the spatial database with the values for the
- Dirichlet boundary condition (
-\family typewriter
-axialdisp.spatialdb
-\family default
-).
+) corresponding to the nodeset in Cubit, and a label to the boundary condition
+ used in any error messages.
\end_layout
\begin_layout Description
-pylithapp.problem.formulation.output.output.writer Gives the base filename for
- VTK output
+pylithapp.problem.formulation.output.domain Gives the base filename for HDF5
+ output
\begin_inset Newline newline
\end_inset
(
\family typewriter
-axialdisp.vtk
+step01.
\family default
-).
+h5).
\end_layout
-\begin_layout Description
-pylithapp.timedependent.materials.material.output Gives the base filename for
- state variable output files (
-\family typewriter
-axialdisp-statevars.vtk
-\family default
-).
-\end_layout
-
\begin_layout Standard
-The values for the Dirichlet boundary condition are given in the file
-\family typewriter
-axialdisp.spatialdb
-\family default
-, as specified in
-\family typewriter
-axialdisp.cfg
-\family default
-.
- The format of all spatial database files is similar.
- In this case, the desired displacement values are given at two points (lower
- left and upper right).
- Since data are being specified at points (rather than being uniform over
- the mesh, for example), the data dimension is one.
+We run this example by typing
\end_layout
-\begin_layout Standard
-The files containing common information (
-\family typewriter
-twotri3.mesh
-\family default
-,
-\family typewriter
-pylithapp.cfg
-\family default
-,
-\family typewriter
-matprops.spatialdb
-\family default
-) along with the problem-specific files (
-\family typewriter
-axialdisp.cfg
-\family default
-,
-\family typewriter
-axialdisp.spatialdb
-\family default
-) provide a complete description of the problem, and we can then run this
- example by typing
-\end_layout
-
\begin_layout LyX-Code
pylith step01.cfg
\end_layout
\begin_layout Standard
-Once the problem has run, three files will be produced.
- The first file is named
-\family typewriter
-axialdisp_t0000000.vtk
-\family default
-.
- The
-\family typewriter
-t0000000
-\family default
- indicates that the output is for the first (and only) time step, corresponding
- to an elastic solution.
- This file contains mesh information as well as displacement values at the
- mesh vertices.
- The second file is named
-\family typewriter
-axialdisp-statevars_t0000000.vtk
-\family default
-.
- This file contains the state variables for each cell.
- The default fields are the total strain and stress fields.
- Since the cells are linear triangles, there is a single quadrature point
- for each cell and thus a single set of stress and strain values for each
- cell.
- The final file (
-\family typewriter
-axialdisp-statevars_info.vtk
-\family default
-) gives the material properties used for the problem.
- Since we have not specified which properties to write, the default properties
- (
-\family typewriter
-mu
-\family default
-,
-\family typewriter
-lambda
-\family default
-,
-\family typewriter
-density
-\family default
-) are written.
- All of the
-\family typewriter
-.vtk
-\family default
- files may be used with a number of visualization packages.
- If the problem ran correctly, you should be able to generate a figure such
- as Figure
+The problem will produce twelve pairs of HDF5/Xdmf files.
+ The HDF5 files contain the data and the Xdmf files contain the metadata
+ required by ParaView and Visit (and possibly other visualization tools
+ that use Xdmf files) to access the mesh and data sets in the HDF5 files.
+ The files include the solution over the domain and ground surface, the
+ stress and strain within each material, and the fault slip.
+ Figure
\begin_inset CommandInset ref
-LatexCommand vref
+LatexCommand ref
reference "fig:tutorial:subduction:step01"
\end_inset
-, which was generated using ParaView.
+, which was created using ParaView, displays the magnitude of the displacement
+ field with the deformation exaggerated by a factor of 1000.
\end_layout
\begin_layout Standard
@@ -635,7 +667,7 @@
\begin_layout Plain Layout
\align center
\begin_inset Graphics
- filename figs/axialdisp.jpg
+ filename figs/step01_soln.png
lyxscale 50
scale 33
@@ -648,8 +680,9 @@
\begin_inset Caption
\begin_layout Plain Layout
-Color contours and vectors of displacement for the axial displacement example
- using a mesh composed of two linear triangular cells.
+The colors indicate the magnitude of the displacement and the deformation
+ is exaggerated by a factor of 1000.
+
\begin_inset CommandInset label
LatexCommand label
name "fig:tutorial:subduction:step01"
@@ -674,7 +707,10 @@
\end_layout
\begin_layout Standard
-The next example problem is shearing of the mesh in the y direction using
+In this example we simulated the interseismic deformation associated with
+ the oceanic crust subducting beneath the contiental crust and into the
+ mantle.
+ The next example problem is shearing of the mesh in the y direction using
displacements applied along the positive and negative x boundaries.
Parameter settings that augment those in
\family typewriter
Modified: short/3D/PyLith/trunk/examples/2d/subduction/geometry.jou
===================================================================
--- short/3D/PyLith/trunk/examples/2d/subduction/geometry.jou 2011-06-12 02:11:10 UTC (rev 18591)
+++ short/3D/PyLith/trunk/examples/2d/subduction/geometry.jou 2011-06-12 03:43:50 UTC (rev 18592)
@@ -118,6 +118,9 @@
# ----------------------------------------------------------------------
# Split curves to form bounding curves for each material
+#
+# Constructing the entire boundary curves as splines and then breaking
+# them into pieces bounding the surfaces preserves continuity in slip.
# ----------------------------------------------------------------------
split curve topobathy crossing curve slabtop
split curve slabtop crossing curve conmoho
@@ -150,6 +153,10 @@
delete vertex all
imprint all
merge all
+
+# We must stitch the surfaces into a single volume in order to split
+# the curves for the purpose of defining the discretization size along
+# various portions of the curves.
stitch volume all
# Split top of slab for fault surface
Modified: short/3D/PyLith/trunk/examples/2d/subduction/mesh_tri3.exo
===================================================================
(Binary files differ)
Modified: short/3D/PyLith/trunk/examples/2d/subduction/pylithapp.cfg
===================================================================
--- short/3D/PyLith/trunk/examples/2d/subduction/pylithapp.cfg 2011-06-12 02:11:10 UTC (rev 18591)
+++ short/3D/PyLith/trunk/examples/2d/subduction/pylithapp.cfg 2011-06-12 03:43:50 UTC (rev 18592)
@@ -138,43 +138,37 @@
[pylithapp.problem.formulation.output.domain]
output_freq = time_step
time_step = 9.99999*year
-writer.time_format = %04.0f
-writer.time_constant = 1.0*year
+writer = pylith.meshio.DataWriterHDF5Mesh
# Ground surface
[pylithapp.problem.formulation.output.subdomain]
label = groundsurf ; Name of CUBIT nodeset for ground surface.
-writer.time_format = %04.0f
-writer.time_constant = 1.0*year
+writer = pylith.meshio.DataWriterHDF5SubMesh
# Materials
[pylithapp.timedependent.materials.continent_crust.output]
cell_filter = pylith.meshio.CellFilterAvgMesh
output_freq = time_step
time_step = 9.99999*year
-writer.time_format = %04.0f
-writer.time_constant = 1.0*year
+writer = pylith.meshio.DataWriterHDF5Mesh
[pylithapp.timedependent.materials.continent_mantle.output]
cell_filter = pylith.meshio.CellFilterAvgMesh
output_freq = time_step
time_step = 9.99999*year
-writer.time_format = %04.0f
-writer.time_constant = 1.0*year
+writer = pylith.meshio.DataWriterHDF5Mesh
[pylithapp.timedependent.materials.ocean_crust.output]
cell_filter = pylith.meshio.CellFilterAvgMesh
output_freq = time_step
time_step = 9.99999*year
-writer.time_format = %04.0f
-writer.time_constant = 1.0*year
+writer = pylith.meshio.DataWriterHDF5Mesh
[pylithapp.timedependent.materials.ocean_mantle.output]
cell_filter = pylith.meshio.CellFilterAvgMesh
output_freq = time_step
time_step = 9.99999*year
-writer.time_format = %04.0f
-writer.time_constant = 1.0*year
+writer = pylith.meshio.DataWriterHDF5Mesh
# ----------------------------------------------------------------------
# PETSc
Modified: short/3D/PyLith/trunk/examples/2d/subduction/step01.cfg
===================================================================
--- short/3D/PyLith/trunk/examples/2d/subduction/step01.cfg 2011-06-12 02:11:10 UTC (rev 18591)
+++ short/3D/PyLith/trunk/examples/2d/subduction/step01.cfg 2011-06-12 03:43:50 UTC (rev 18592)
@@ -115,30 +115,29 @@
# ----------------------------------------------------------------------
# Domain
[pylithapp.problem.formulation.output.domain]
-writer.filename = output/step01.vtk
+writer.filename = output/step01.h5
# Ground surface
[pylithapp.problem.formulation.output.subdomain]
-writer.filename = output/step01-groundsurf.vtk
+writer.filename = output/step01-groundsurf.h5
# Fault
[pylithapp.problem.interfaces.fault.output]
-writer.time_format = %04.0f
-writer.time_constant = 1.0*year
-writer.filename = output/step01-fault.vtk
+writer = pylith.meshio.DataWriterHDF5SubSubMesh
+writer.filename = output/step01-fault.h5
# Materials
[pylithapp.timedependent.materials.continent_crust.output]
-writer.filename = output/step01-concrust.vtk
+writer.filename = output/step01-concrust.h5
[pylithapp.timedependent.materials.continent_mantle.output]
-writer.filename = output/step01-conmantle.vtk
+writer.filename = output/step01-conmantle.h5
[pylithapp.timedependent.materials.ocean_crust.output]
-writer.filename = output/step01-oceancrust.vtk
+writer.filename = output/step01-oceancrust.h5
[pylithapp.timedependent.materials.ocean_mantle.output]
-writer.filename = output/step01-oceanmantle.vtk
+writer.filename = output/step01-oceanmantle.h5
# End of file
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